So I just reinstalled oblivion and obviously added some mods... Load up the game, start a new file and for some reason all of the original races in the game have no eyes, and races added by mods have duplicates, one with eyes and another without eyes. This is my modlist:

Oblivion.esmUnofficial Shivering Isles Patch.espYou Are Here.esmAmbientDungeons.espOblivion Graphics Extender Support.espStreamline 3.1.espEnhanced Hotkeys.espMaleBodyReplacerV4.espBeautiful People.espBeautiful PeopleV22 - MaleReplacerV4.espDLCHorseArmor.espDLCOrrery.espDLCFrostcrag.espDLCThievesDen.espDLCVileLair.espDLCMehrunesRazor.espDLCSpellTomes.espKnights.espDLCShiveringIsles.esp

Any help on what the problem is would be appreciated.

It has to be one of these 3:

MaleBodyReplacerV4.esp
Beautiful People.esp
Beautiful PeopleV22 - MaleReplacerV4.esp

De-activate and check! I'm guessing most probably #1 and #3 above are alternates...

Don't use BP-RM compatibility plugin(unless you installed Elaborate Eyes as well). Instead, use Wrye Bash to make a merged patch if possible, or make your own merged plugin with TES4Edit or TES4Gecko.

Well, I just tried that....Now it won't let me deactivate the compatibility plugin because it's a master file to the bashed patch?

You have to build bashed patch without activating BP-RM compatiblity plugin. Or, make a merged plugin by merging BP plugin and RM plugin with TES4Edit or TES4Gecko, then use merged one.